redo README.Rmd and .md

README.Rmd

@@ -20,11 +20,15 @@ sigmoid
 [![Total RStudio Cloud Downloads](http://cranlogs.r-pkg.org/badges/grand-total/sigmoid?color=brightgreen)](https://cran.r-project.org/package=sigmoid)
 [![RStudio Cloud Downloads](http://cranlogs.r-pkg.org/badges/sigmoid?color=brightgreen)](https://cran.r-project.org/package=sigmoid)
 [![Travis-CI Build Status](https://travis-ci.org/bquast/sigmoid.svg?branch=master)](https://travis-ci.org/bquast/sigmoid)
-[![Coverage Status](https://img.shields.io/coveralls/bquast/sigmoid.svg)](https://coveralls.io/r/bquast/sigmoid?branch=master)
+[![Coverage Status](https://coveralls.io/repos/github/bquast/sigmoid/badge.svg?branch=master)](https://coveralls.io/github/bquast/sigmoid?branch=master)
 -->
 
 Several different sigmoid functions are implemented, including a wrapper function, SoftMax preprocessing and inverse functions.
 
+Demonstration
+---------------
+![sigmoid demonstration](/man/figures/sigmoid.gif)
+
 Installation
 ------------
 The **stable** version can be installed from [CRAN](https://cran.r-project.org/package=sigmoid) using:

README.md

@@ -1,42 +1,48 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-sigmoid
-=======
+
+# sigmoid
+
+<!--
 [![License](http://img.shields.io/badge/license-GPLv3-brightgreen.svg)](http://www.gnu.org/licenses/gpl-3.0.html)
 [![CRAN Version](http://www.r-pkg.org/badges/version/sigmoid)](https://cran.r-project.org/package=sigmoid)
 [![Total RStudio Cloud Downloads](http://cranlogs.r-pkg.org/badges/grand-total/sigmoid?color=brightgreen)](https://cran.r-project.org/package=sigmoid)
 [![RStudio Cloud Downloads](http://cranlogs.r-pkg.org/badges/sigmoid?color=brightgreen)](https://cran.r-project.org/package=sigmoid)
 [![Travis-CI Build Status](https://travis-ci.org/bquast/sigmoid.svg?branch=master)](https://travis-ci.org/bquast/sigmoid)
-[![Coverage Status](https://img.shields.io/coveralls/bquast/sigmoid.svg)](https://coveralls.io/r/bquast/sigmoid?branch=master)
+[![Coverage Status](https://coveralls.io/repos/github/bquast/sigmoid/badge.svg?branch=master)](https://coveralls.io/github/bquast/sigmoid?branch=master)
+-->
+
+Several different sigmoid functions are implemented, including a wrapper
+function, SoftMax preprocessing and inverse functions.
 
-Several different sigmoid functions are implemented, including a wrapper function, SoftMax preprocessing and inverse functions.
+## Demonstration
 
-Demonstration
----------------
 ![sigmoid demonstration](/man/figures/sigmoid.gif)
 
-Installation
-------------
+## Installation
 
-The **stable** version can be installed from [CRAN](https://cran.r-project.org/package=sigmoid) using:
+The **stable** version can be installed from
+[CRAN](https://cran.r-project.org/package=sigmoid) using:
 
 ``` r
 install.packages('sigmoid')
 ```
 
-The **development** version, to be used **at your peril**, can be installed from [GitHub](http://github.com/bquast/sigmoid) using the `devtools` package.
+The **development** version, to be used **at your peril**, can be
+installed from [GitHub](http://github.com/bquast/sigmoid) using the
+`devtools` package.
 
 ``` r
 if (!require('devtools')) install.packages('devtools')
 devtools::install_github('bquast/sigmoid')
 ```
 
-Usage
------
+## Usage
 
 Following installation, the package can be loaded using:
 
-The `sigmoid()` function returns the sigmoid value of the input(s), by default this is done using the **standard logistic function**.
+The `sigmoid()` function returns the sigmoid value of the input(s), by
+default this is done using the **standard logistic function**.
 
 ``` r
 library(sigmoid)
@@ -48,17 +54,17 @@ Inputs can also be tensors, such as vectors, matrices, or arrays.
 
 ``` r
 sigmoid(-5:5)
-#>  [1] 0.006692851 0.017986210 0.047425873 0.119202922 0.268941421
-#>  [6] 0.500000000 0.731058579 0.880797078 0.952574127 0.982013790
-#> [11] 0.993307149
+#>  [1] 0.006692851 0.017986210 0.047425873 0.119202922 0.268941421 0.500000000
+#>  [7] 0.731058579 0.880797078 0.952574127 0.982013790 0.993307149
 sigmoid( matrix(-3:5,nrow=3) ) # etc.
 #>            [,1]      [,2]      [,3]
 #> [1,] 0.04742587 0.5000000 0.9525741
 #> [2,] 0.11920292 0.7310586 0.9820138
 #> [3,] 0.26894142 0.8807971 0.9933071
 ```
 
-The `sigmoid()` function is a wrapper, which by default uses the `logistic()` function, it can also use other methods.
+The `sigmoid()` function is a wrapper, which by default uses the
+`logistic()` function, it can also use other methods.
 
 ``` r
 sigmoid( -5:5, method='Gompertz' )
@@ -89,34 +95,34 @@ ggplot(df, aes(input, logistic(input))) + geom_line() +
   geom_line(aes(input,Gompertz(input)), colour='red')
 ```
 
-![](tools/sigmoid-shape-1.png)
+![](tools/sigmoid-shape-1.png)<!-- -->
 
 For inverses, additional parameters, SoftMax, etc. see the vignette.
 
     vignette('sigmoid')
 
-For general information on using the package, please refer to the help files.
+For general information on using the package, please refer to the help
+files.
 
 ``` r
 help('sigmoid')
 help(package='sigmoid')
 ```
 
-Additional Information
-----------------------
+## Additional Information
 
 An overview of the changes is available in the NEWS file.
 
 ``` r
 news(package='sigmoid')
 ```
 
-There is a dedicated website with information hosted on my [personal website](http://qua.st/).
+There is a dedicated website with information hosted on my [personal
+website](http://qua.st/).
 
 <http://qua.st/sigmoid>
 
-Development
------------
+## Development
 
 Development takes place on the GitHub page.